I think a good solution would be to persuade the sales to include PCI as an "expensive option". Warn them about disadvantages, suggest making 2 versions (one just based on 3rd party media converter and one on PCI) and let the customer choose (and get some man hours of work for yourself to design the PCI card nobody will buy anyway)

If they want to be really "modern and trendy" suggest making the readers "internet-aware" and communicate with the PC over Ethernet LAN. :)
Of course that presents even more security challenges, but if they are willing to throw enough money at them, it will be better if they design something new than invest in design based on obsolete technology.